I just got my protein identification report. What does the Mascot Score mean?
The Protein Identification report contains a list of proteins that have been positively identified by a significant Mascot Score in the Mascot database search [1, 2].
For protein identification, the protein is typically cleaved by trypsin and the resulting peptides analyzed by nanoLC-MS/MS. The mass spectrometric data contain a list of the accurate peptide masses and peptide fragment masses. These are searched against sequence databases containing known protein amino acid sequences using the Mascot database search software. The Mascot Score is a statistical score for how well the experimental data match the database sequence [1, 2].
What makes a positive Mascot Protein identification?
The Mascot score for a protein is the summed score for the individual peptides, e.g. peptide masses and peptide fragment ion masses, for all peptides matching a given protein. For a positive protein identification, the mascot score has to be above the 95% confidence level. For a database search in the nrbd protein database from NCBI containing 18 million known protein sequence, the 95% confidence level is around a Score of 90 [1, 2].
The Mascot score is a logarithmic scoring and is described in detail at the Matrix Science website (http://www.matrixscience.com/).
If you want to learn more about mass spectrometric identification of proteins from 1D and 2D gels using mass spec, read here:Protein Identification
 Perkins et al: “Probability-based protein identification by searching sequence databases using mass spectrometry data“, Electrophoresis, 1999
 Koenig et al: “Robust prediction of the MASCOT score for an improved quality assessment in mass spectrometric proteomics.“, Journal of Proteome Research, 2008